Novel therapeutic agents that modulate enzymatic processes

Abstract

Novel multi-binding compounds are disclosed that modulate enzymatic processes. The compounds of the invention comprise from 2-10 ligands covalently connected, each of said ligands being capable of binding to an enzyme, enzyme substrate or enzyme cofactor thereby modulating the biological processes/functions thereof.

It is claimed:  
     
         1 . A multibinding compound of the formula: 
       (L) p X q   Formula I 
       in which 
 L is a ligand that may be the same or different at each occurrence;  
 X is a linker that may be the same or different at each occurrence;  
 p is an integer of 2-10; and  
 q is an integer of 1-20,  
 each of said ligands compromising a ligand domain capable of binding to an enzyme, enzyme substrate, or enzyme cofactors;  
 or a pharmceutically acceptable salt thereof;  
 with the proviso that when p is 2 and q is 1 then: 
 when the enzyme is acrosin, the ligand cannot be a benzamidine;  
 when the enzyme is a bacterial transglycosylase, the ligand cannot be a glycopeptide;  
 when the enzyme is bacterial DNA gyrase, the ligand cannot be a quinolone;  
 when the enzyme is thrombin, the ligand cannot be hirudin analogs;  
 when the enzyme is thromboxane synthase, the ligand cannot be dazoxiben or isbogrel;  
 when the enzyme is phosphokinase, the ligand cannot be a cinnamyl derivative;  
 when the enzyme is oxidoreductase, the ligand cannot be 5-aminosalicylic acid;  
 when the enzyme is cholesterol o-acyltransferase, the ligand cannot be a furochromone, a furobenzoxazine, or a benzodifuran;  
 and also with the proviso that;  
 
 the enzyme is not a phosphodiesterase or a penicillin binding protein;  
 the ligand is not cyclosporin, FK506, rapamycin, or rifamycin, or AZT in combination with DDI.  
 
     
     
         2 . The multibinding compound of  claim 1 , wherein p is 2 and q is 1.  
     
     
         3 . The multibinding compound of  claim 2 , wherein the ligands are different.  
     
     
         4 . The multibinding compound of  claim 1 , wherein the linker or linkers employed are selected from the group comprising flexible linkers, rigid linkers, hydrophobic linkers, hydrophilic linkers, linkers of different geometry, acidic linkers, basic linkers, linkers of different polarization and/or polarizability and amphiphilic linkers.  
     
     
         5 . The multibinding compound of  claim 4 , wherein the linkers are selected to have different linker lengths ranging from about 2 to 100 angstroms.  
     
     
         6 . The multibinding compound of  claim 5  wherein the linkers are selected to have different linker lengths ranging from about 3 to 40 angstroms.  
     
     
         7 . The multibinding compound of  claim 1 , wherein the linker is represented by the formula: 
       —X′—Z′—(Y′—Z″) m —Y″—Z′—X′— 
       in which: 
 m is an integer of 0-20;  
 X′ at each separate occurrence is —O—, —S—, —S(O)—, —S(O) 2 —, —NR— (where R is as defined below), —C(O)—, or a covalent bond;  
 Z′ and Z″ at each separate occurrence are alkylene, cycloalkylene, alkenylene, alkynylene, arylene, heteroarylene, heterocycloalkylene, or a covalent bond;  
 Y′ and Y″ at each separate occurrence are:  
                     
  —O—Z′—O—, —N(R)—Z′—N(R), —S—S—, or a covalent bond; in which: 
 n is 0, 1 or 2; and  
 R, R′ and R″ at each separate occurrence are chosen from hydrogen, alkyl, cycloalkyl, alkenyl, cycloalkenyl, alkynyl, aryl, heteroaryl, and heterocyclo.  
 
 
     
     
         8 . The multibinding compound of  claim 2 , wherein the ligands are the same.  
     
     
         9 . The multibinding compound of  claim 8 , wherein the two ligands are covalently linked to the linker at the same point of the ligand.  
     
     
         10 . The multibinding compound of  claim 9 , wherein the two ligands are covalently linked to the linker at different points on the ligand.  
     
     
         11 . A pharmaceutical composition comprising a therapeutically effective amount of a multibinding compound of  claim 1 , or a pharmaceutically acceptable salt thereof; admixed with at least one pharmaceutically acceptable excipient.  
     
     
         12 . A method for treating a disease or condition in a mammalian or avian subject which is alleviated by treatment with a multibinding agent, comprising administering to a subject in need of such treatment a therapeutically effective amount of a multibinding compound of  claim 1 , or a pharmaceutically acceptable salt thereof.  
     
     
         13 . The method of  claim 12 , wherein the method is chosen from treatment of a mammal afflicted with pathogenic bacteria, psoriasis, multiple sclerosis, rheumatoid arthritis, insulin-dependent diabetes, breast cancer and prostate cancer, disease states related to blood clotting, Parkinson's disease, transplant rejection, T-cell leukemia, or lymphoma, arthritis, metastatic cancer, tumor growth related to metalloprotease enzymes, stress and hypertension.  
     
     
         14 . A method for identifying multimeric ligand compounds that possess multibinding properties with respect to enzymes, which method comprises: 
 (a) identifying a ligand or mixture of ligands capable of binding to an enzyme and having at least one chemically reactive functional group;    (b) identifying a library of linkers wherein each linker in said library comprises at least two functional groups having complementary chemical activity to at least one of the ligand functional groups;    (c) preparing a multimeric ligand compound by combining the ligand or ligands identified in step (a) with the library of linkers identified in step (b) under conditions sufficient to form covalent linkages between the complementary functional groups of the ligand or ligands and the linker;and    (d) assaying the multimeric ligand compound library produced in step (c) to identify multimeric ligand compounds that possess multibinding properties.    
     
     
         15 . A method for identifying multimeric ligand compounds that possess multibinding properties with respect to enzymes, which method comprises: 
 (e) identifying a ligand or mixture of ligands capable of binding to an enzyme and having at least one chemically reactive functional group;    (f) identifying a linker or mixture of linkers wherein each linker comprises at least two functional groups having complementary chemical activity to at least one of the ligand functional groups;    (g) preparing a multimeric ligand compound by combining the ligand or ligands identified in step (a) with the library of linkers identified in step (b) under conditions sufficient to form covalent linkages between the complementary functional groups of the ligand or ligands and the linker; and    (h) assaying the multimeric ligand compound library produced in step (c) to identify multimeric ligand compounds that possess multibinding properties.    
     
     
         16 . The method of  claim 14  or  15 , wherein the preparation of the multimeric ligand compound library is achieved by either the sequential or concurrent combination of the two or more stoichiometric equivalents of the ligands identified in (a) with the linkers identified in (b).  
     
     
         17 . The method of  claim 16 , wherein the multimeric ligand compounds comprising the multimeric ligand compound library are dimeric.  
     
     
         18 . The method of  claim 17 , wherein each member of the library is isolated and identified by preparative liquid chromatography mass spectrometry (LCMS).  
     
     
         19 . The method of  claim 18 , wherein the linker or linkers employed are selected from the group comprising flexible linkers, rigid linkers, hydrophobic linkers, hydrophilic linkers, linkers of different geometry, acidic linkers, basic linkers, linkers of different polarization and/or polarizability and amphiphilic linkers.  
     
     
         20 . The method of  claim 19 , wherein the linkers comprise linkers of different chain length and/or having different complementary reactive groups.  
     
     
         21 . The method of  claim 20 , wherein the linkers are selected to have different linker lengths ranging from about 2 to 100 angstroms.  
     
     
         22 . The method of  claim 14  or  15 , wherein said reactive functional groups of ligands is selected from the group consisting of carboxylic acids, carboxylic acid halides, carboxyl esters, amines, halides, pseudohalides, isocyanates, vinyl unsaturation, ketones, aldehydes, thiols, alcohols, anhydrides, boronates, and precursors thereof, wherein the reactive functionality on the ligand is selected to be complementary to at least one of the reactive groups on the linker so that a covalent linkage can be formed between the linker and the ligand.  
     
     
         23 . A library of multimeric ligand compounds which may possess multivalent properties, which library is prepared by the method comprising: 
 (a) identifying a library of ligands, wherein each ligand contains at least one reactive functionality;    (b) identifying a linker or mixture of linkers wherein each linker comprises at least two functional groups having complementary reactivity to at least one of the reactive functional groups of the ligand; and    (c) preparing a multimeric ligand compound library by combining at least two stoichiometric equivalents of the library of ligands identified in (a) with the linker or mixture of linkers identified in (b) under conditions wherein the complementary functional groups react to form a covalent linkage between said linker and at least two of said ligands.    
     
     
         24 . The library of  claim 23 , wherein the linker or linkers employed are selected from the group comprising flexible linkers, rigid linkers, hydrophobic linkers, hydrophilic linkers, linkers of different geometry, acidic linkers, basic linkers, linkers of different polarization and/or polarizability and amphiphilic linkers.  
     
     
         25 . The library of  claim 24 , wherein the linkers comprise linkers of different chain length and/or having different complementary reactive groups.  
     
     
         26 . The library of  claim 25 , wherein the linkers are selected to have different linker lengths ranging from about 2 to 100 angstroms.  
     
     
         27 . The library of  claim 23 , wherein the ligand or mixture of ligands is selected to have reactive functionality at different sites on said ligands.  
     
     
         28 . The library of  claim 27 , wherein said reactive functionality is selected from the group consisting of carboxylic acids, carboxylic acid halides, carboxyl esters, amines, halides, pseudohalides, isocyanates, vinyl unsaturation, ketones, aldehydes, thiols, alcohols, anhydrides, boronates, and precursors thereof wherein the reactive functionality on the ligand is selected to be complementary to at least one of the reactive groups on the linker so that a covalent linkage can be formed between the linker and the ligand.  
     
     
         29 . The library of  claim 23 , wherein the multimeric ligand compound library comprises homomeric ligand compounds.  
     
     
         30 . The library of  claim 23 , wherein the multimeric ligand compound library comprises heteromeric ligand compounds.  
     
     
         31 . An iterative method for identifying multimeric ligand compounds possessing multibinding properties which method comprises: 
 (a) preparing a first collection or iteration of multimeric compounds which is prepared by contacting at least two stoichiometric equivalents of a ligand or mixture of ligands which target a receptor with a linker or mixture of linkers wherein said ligand or mixture of ligands comprises at least one reactive functionality and said linker or mixture of linkers comprises at least two functional groups having complementary reactivity to at least one of the reactive functional groups of the ligand wherein said contacting is conducted under conditions wherein the complementary functional groups react to form a covalent linkage between said linker and at least two of said ligands;    (b) assaying said first collection or iteration of multimeric compounds to assess which if any of said multimeric compounds possess multibinding properties;    (c) repeating the process of (a) and (b) above until at least one multimeric compound is found to possess multibinding properties;    (d) evaluating what molecular constraints imparted or are consistent with imparting multibinding properties to the multimeric compound or compounds found in the first iteration recited in (a)-(c) above;    (e) creating a second collection or iteration of multimeric compounds which elaborates upon the particular molecular constraints imparting multibinding properties to the multimeric compound or compounds found in said first iteration;    (f) evaluating what molecular constraints imparted or are consistent with imparting enhanced multibinding properties to the multimeric compound or compounds found in the second collection or iteration recited in (e) above;    (g) optionally repeating steps (e) and (f) to further elaborate upon said molecular constraints.    
     
     
         32 . The method of  claim 31 , wherein steps (e) and (f) are repeated from 2-50 times.  
     
     
         33 . The method of  claim 32 , wherein steps (e) and (f) are repeated from 5-50 times.